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Breast Cancer Gene Expression Data from Frankfurt Series


ABSTRACT: Pooling of microarray datasets seems to be a reasonable approach to increase sample size when a heterogeneous disease like breast cancer is concerned. Different methods for the adaption of datasets have been used in the literature. We have analyzed influences of these strategies using a pool of 3,030 Affymetrix U133A microarrays from breast cancer samples. We present data on the resulting concordance with biochemical assays of well known parameters and highlight critical pitfalls. We further propose a method for the inference of cutoff values directly from the data without prior knowledge of the true result. The cutoffs derived by this method displayed high specificity and sensitivity. Markers with a bimodal distribution like ER, PgR, and HER2 discriminate different biological subtypes of disease with distinct clinical courses. In contrast, markers displaying a continuous distribution like proliferation markers as Ki67 rather describe the composition of the mixture of cells in the tumor. Fresh frozen surgical biopsy samples from consecutive patients were analyzed on Affymetrix HGU133A

ORGANISM(S): Homo sapiens

SUBMITTER: Thomas Karn 

PROVIDER: E-GEOD-4611 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Data-driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer.

Karn Thomas T   Metzler Dirk D   Ruckhäberle Eugen E   Hanker Lars L   Gätje Regine R   Solbach Christine C   Ahr Andre A   Schmidt Marcus M   Holtrich Uwe U   Kaufmann Manfred M   Rody Achim A  

Breast cancer research and treatment 20090520 3


Pooling of microarray datasets seems to be a reasonable approach to increase sample size when a heterogeneous disease like breast cancer is concerned. Different methods for the adaption of datasets have been used in the literature. We have analyzed influences of these strategies using a pool of 3,030 Affymetrix U133A microarrays from breast cancer samples. We present data on the resulting concordance with biochemical assays of well known parameters and highlight critical pitfalls. We further pro  ...[more]

Publication: 1/5

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